+ </mappingSet>
+ </axis-wsdl2java>
+ </target>
+
+ <target name="makedist" depends="build, buildPropertiesFile, buildindices">
+ <!-- make the package jar -->
+ <mkdir dir="${packageDir}"/>
+
+ <jar destfile="${packageDir}/${outputJar}">
+ <manifest>
+ <attribute name="Main-Class" value="jalview.bin.Jalview"/>
+ </manifest>
+ <fileset dir="${outputDir}/">
+ <exclude name="cache*/**"/>
+ <exclude name="*.jar" />
+ <exclude name="*.jar.*" />
+ <exclude name="**/*.jar" />
+ <exclude name="**/*.jar.*" />
+ </fileset>
+ </jar>
+
+ <copy toDir="${packageDir}" flatten="true">
+ <fileset dir="${outputDir}">
+ <include name="*.jar"/>
+ <include name="**/*.jar"/>
+ </fileset>
+ </copy>
+ </target>
+
+
+ <!-- jalopy code reformatter -->
+ <target name="sourcescrub" depends="init,build">
+ <jalopy destdir="jsrc" classpathref="run.classpath"
+ convention="jalview-jalopy.xml">
+ <fileset dir="${sourceDir}">
+ <include name="*.java"/>
+ <include name="**/*.java"/>
+ <include name="**/**/*.java"/>
+ </fileset>
+ </jalopy>
+ </target>
+
+
+
+ <!-- Compile, package and obfuscate Jalview Applet -->
+ <target name="makeApplet" depends="obfuscate"/>
+
+ <target name="compileApplet" depends="init,clean">
+ <mkdir dir="${outputDir}"/>
+ <javac source="1.5"
+ target="1.5"
+ srcdir="${sourceDir}"
+ destdir="${outputDir}"
+ debug="${javac.debug}"
+ classpath="appletlib/${jmolJar}"
+ includes="jalview/appletgui/**"
+ excludes="ext/**,MCview/**,org/**,vamsas/**"
+ />
+ </target>
+
+ <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
+ <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif"/>
+ <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif"/>
+ <jar destfile="in.jar">
+ <manifest>
+ <attribute name="Main-Class" value="jalview.bin.JalviewLite"/>
+ </manifest>
+ <fileset dir="${outputDir}">
+ <include name="com/**"/>
+ <include name="MCview/**"/>
+ <include name="jalview/**"/>
+ <include name=".build_properties"/>
+ <include name="images/idwidth.gif"/>
+ <include name="images/link.gif"/>
+ </fileset>
+ </jar>
+ </target>
+ <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally" description="construct the final jalviewLite applet jar with or without obfuscation">
+ </target>
+ <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
+ <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true"/>
+ <delete file="in.jar"/>
+ </target>
+ <target name="-obfuscatereally" unless="donotobfuscate">
+
+ <path id="obfuscateDeps.path">
+ <pathelement location="${applet.jre.tools}"/>
+ <pathelement location="appletlib/${jmolJar}"/>
+ </path>
+ <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
+
+ <proguard>
+ <injar file="in.jar"/>
+ <outjar file="${jalviewLiteJar}"/>
+ <libraryjar refid="obfuscateDeps.path"/>
+ <keep access="public" type="class"
+ name="jalview.bin.JalviewLite">
+ <field access="public"/>
+ <method access="public"/>
+ <constructor access="public"/>
+ </keep>
+ <!-- -libraryjars "${obfuscateDeps}"
+ -injars in.jar
+ -outjars jalviewApplet.jar
+ -keep public class jalview.bin.JalviewLite
+ { public * ; } -->
+ </proguard>
+ <delete file="in.jar"/>
+ </target>
+
+ <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
+ <taskdef name="castor-srcgen"
+ classname="org.castor.anttask.CastorCodeGenTask"
+ classpathref="build.classpath" />
+ <delete>
+ <fileset dir="${sourceDir}/jalview/schemabinding/version2">
+ <include name="*.java"/>
+ <include name="descriptors/*.java"/>
+ </fileset>
+ </delete>
+ <castor-srcgen file="${schemaDir}/vamsas.xsd"
+ todir="${sourceDir}"
+ package="jalview.schemabinding.version2"
+ warnings="false"
+ nodesc="false"
+ verbose="true"
+ properties="${schemaDir}/jalview.properties"
+ />
+ <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd"
+ todir="${sourceDir}"
+ package="jalview.schemabinding.version2"
+ warnings="false"
+ nodesc="false"
+ verbose="true"
+ properties="${schemaDir}/jalview.properties"
+ />
+ <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd"
+ todir="${sourceDir}"
+ package="jalview.schemabinding.version2"
+ warnings="false"
+ nodesc="false"
+ verbose="true"
+ properties="${schemaDir}/jalview.properties"
+ />
+ <castor-srcgen file="${schemaDir}/jalview.xsd"
+ todir="${sourceDir}"
+ package="jalview.schemabinding.version2"
+ warnings="false"
+ nodesc="false"
+ verbose="true"
+ properties="${schemaDir}/jalview.properties"
+
+ />
+ <!--
+ now build the jalview.binding package with the old schema set
+ -->
+ <delete>
+ <fileset dir="${sourceDir}/jalview/binding/">
+ <include name="**"/>
+ </fileset>
+ </delete>
+ <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd"
+ todir="${sourceDir}"
+ package="jalview.binding"
+ warnings="false"
+ nodesc="true"
+ verbose="true"
+ properties="${schemaDir}/jalview.nodesc.properties"
+ />
+ <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd"
+ todir="${sourceDir}"
+ package="jalview.binding"
+ warnings="false"
+ nodesc="true"
+ verbose="true"
+ properties="${schemaDir}/jalview.nodesc.properties"
+ />
+ <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd"
+ todir="${sourceDir}"
+ package="jalview.binding"
+ warnings="false"
+ nodesc="true"
+ verbose="true"
+ properties="${schemaDir}/jalview.nodesc.properties"
+ />
+ </target>
+ <target name="sourcedist" description="create jalview source distribution" depends="init">
+ <delete file="${source.dist.name}"/>
+ <tar destfile="${source.dist.name}" compression="gzip">
+ <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
+ <include name="LICENSE"/>
+ <include name="README"/>
+ <include name="build.xml"/>
+ <include name="jalview-jalopy.xml"/>
+ <include name="JalviewApplet.jpx"/>
+ <include name="JalviewX.jpx"/>
+ <include name="${sourceDir}/*.java"/>
+ <include name="${sourceDir}/**/*.java"/>
+ <include name="${sourceDir}/**/*.cdr"/>
+ <include name="${libDir}/**/*"/>
+ <include name="${resourceDir}/**/*"/>
+ <include name="${helpDir}/**/*"/>
+ <include name="appletlib/${jmolJar}"/>
+ <exclude name="**/*locales"/>
+ <exclude name="*locales/**"/>
+ <exclude name="utils/InstallAnywhere/**Build.iap_xml"/>
+ <exclude name="utils/InstallAnywhere/**Build*/**"/>
+ <exclude name="utils/InstallAnywhere/**Build*/**"/>
+ <exclude name="utils/InstallAnywhere/**locale*"/>
+ <exclude name="utils/InstallAnywhere/**locale*/**"/>
+ <include name="${schemaDir}/**/*"/>
+ <include name="utils/**/*"/>
+ <include name="${docDir}/**/*"/>
+ </tarfileset>
+ </tar>
+ </target>
+ </project>